Neurobiological theories suggest that inter-individual differences in vagally mediated heart rate variability (vmHRV) have the potential to serve as a biomarker for inter-individual differences in emotion regulation that are due to inter-individual differences regarding the engagement of prefrontal and (para-)limbic brain regions during emotion processing. To test these theories, we investigated whether inter-individual differences in vmHRV would be associated with inter-individual differences in emotion regulation. We determined resting state vmHRV in a sample of 176 individuals that had also completed a short self-report measure of reappraisal and suppression use. Resting state vmHRV was derived from short-term (300 s) and ultra-short-term (120 s, 60 s) recordings of participants’ heart rate to determine the robustness of possible findings. Irrespective of recording length, we found that an increase in resting state vmHRV was associated with an increase in self-reported reappraisal but not suppression use. However, this association was only evident among male but not female participants, indicating a sex-specific association between inter-individual differences in resting state vmHRV and inter-individual differences in self-reported emotion regulation. These findings, which are consistent with previous ones, support theoretical claims that inter-individual differences in vmHRV serve as a biomarker for inter-individual differences in emotion regulation. Combing (ultra-)short-term measures of resting state vmHRV with short self-report measures of emotion regulation may, thus, be useful for researchers who have to investigate the neurobiological mechanisms of emotion regulation in a time- and resource-efficient manner.